Genome-wide analysis of long non-coding RNAs affecting roots development at an early stage in the rice response to cadmium stress

Ghulam Mustafa Wassan,Jie Xu,Haohua He,Xiaotang Sun,Lifang Hu,Hira Khanzada,Junru Fu,Changlan Zhu,Yujin Chen,Xiaosong Peng,Jianmin Bian,Xiaorong Chen,Qiuying Yu,Xiaopeng He,Linjuan Ouyang,Shilai Shi,Liang Chen,Ninfei Jiang

doi:10.1186/s12864-018-4807-6

Ghulam Mustafa Wassan, Jie Xu + Show 16 more

Open Access

https://doi.org/10.1186/s12864-018-4807-6

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Abstract

BackgroundLong non-coding RNAs (lncRNAs) have been found to play a vital role in several gene regulatory networks involved in the various biological processes in plants related to stress response. However, systematic analyses of lncRNAs expressed in rice Cadmium (Cd) stress are seldom studied. Thus, we presented the characterization and expression of lncRNAs in rice root development at an early stage in response to Cd stress.ResultsThe lncRNA deep sequencing revealed differentially expressed lncRNAs among Cd stress and normal condition. In the Cd stress group, 69 lncRNAs were up-regulated and 75 lncRNAs were down-regulated. Furthermore, 386 matched lncRNA-mRNA pairs were detected for 120 differentially expressed lncRNAs and 362 differentially expressed genes in cis, and target gene-related pathway analyses exhibited significant variations in cysteine and methionine metabolism pathway-related genes. For the genes in trans, overall, 28,276 interaction relationships for 144 lncRNAs and differentially expressed protein-coding genes were detected. The pathway analyses found that secondary metabolites, such as phenylpropanoids and phenylalanine, and photosynthesis pathway-related genes were significantly altered by Cd stress. All of these results indicate that lncRNAs may regulate genes of cysteine-rich peptide metabolism in cis, as well as secondary metabolites and photosynthesis in trans, to activate various physiological and biochemical reactions to respond to excessive Cd.ConclusionThe present study could provide a valuable resource for lncRNA studies in response to Cd treatment in rice. It also expands our knowledge about lncRNA biological function and contributes to the annotation of the rice genome.

Highlights

Long non-coding RNAs have been found to play a vital role in several gene regulatory networks involved in the various biological processes in plants related to stress response
The trans role of Long non-coding RNAs (lncRNAs) in target genes On the other hand, we examined the trans role of 143 lncRNAs genes on the basis of its expressed correlation coefficient (Pearson correlation ≥0.95 or ≤ − 0.95)
Our data systemically predict the lncRNAs at the whole transcriptome level and showed that which specific lncRNAs seek out selective sites in the genome for interaction in rice Cd stress

Summary

Introduction

Long non-coding RNAs (lncRNAs) have been found to play a vital role in several gene regulatory networks involved in the various biological processes in plants related to stress response. Long noncoding RNAs (lncRNAs) are a diverse class of molecules derived from RNA polymerases and arise as important regulators in the regulation of gene expression and transcription in animals and plants [1]. LncRNAs are clearly distinguishable from mRNAs in their sequence structure, expression level, positional characteristics and evolution conservation [3,4,5]. Their subspecies have been characterized and categorized in humans [3, 6], Caenorhabditis elegans [7] and zebrafish [8]. Nuclear speckle RNA-binding proteins (NSRs), together with AS competitor long

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